Faculty Publications
Faculty ↓
Armache
Arora
Belasco
Bonneau
Brujic
Cardozo
Dustin
Hubbard
Krogsgaard
Kong
Mohammadi
Neubert
Nudler
Rothenberg
Seeman
Serganov
Stokes
Traaseth
Turnbull
Wang
Zhang
The Neubert lab has developed the method of Stable Isotope Labeling by Amino Acids in Cell culture (SILAC). This method has been used to study brain-derived neurotrophic factor (BDNF) signaling in a differentiated, non-dividing cell type such as primary neurons. A review describing this method has been published in Methods Mol Biol. 527:79 (2009).
Karim-Jean Armache:
Armache KJ, Garlick JD, Canzio D, Narlikar GJ, and Kingston RE. Structural Basis of Silencing: Sir3 BAH Domain in Complex with a Nucleosome at 3.0 Å Resolution. Science. 334:977-82. (2011)
Kostrewa, D, Zeller, ME, Armache, KJ, Seizl, M, Leike, K, Thomm, M, and Cramer, P. RNA Polymerase II-TFIIB Structure and Mechanism of Transcription Initiation. Nature. 462:323-330. (2009)
Brueckner F, Armache KJ, Cheung A, Damsma GE, Kettenberger H, Lehmann E, Sydow J,
and Cramer P. Structure-Function Studies of the RNA Polymerase II Elongation Complex. Acta Crystallogr D Biol Crystallogr. 65:112-120. (2009)
Paramjit Arora:
Jespersen C, Soragni E, James Chou C, Arora PS, Dervan PB, Gottesfeld JM. Chromatin structure determines accessibility of a hairpin polyamide-chlorambucil conjugate at histone H4 genes in pancreatic cancer cells. Bioorg Med Chem Lett. 22:4068-71. (2012)
Mahon AB, Arora PS. Design, synthesis and protein-targeting properties of thioether-linked hydrogen bond surrogate helices. Chem Commun. 48:1416-8. (2012)
Bullock BN, Jochim AL, Arora PS. Assessing helical protein interfaces for inhibitor design. J Am Chem Soc. 133:14220-3. (2011)
Patgiri A, Yadav KK, Arora PS, Bar-Sagi D. An orthosteric inhibitor of the Ras-Sos interaction. Nat Chem Biol. 7:585-7. (2011)
Patgiri A, Menzenski MZ, Mahon AB, Arora PS. Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach. Nat Protoc. 5:1857-65. (2010)
Guarracino DA, Bullock BN, Arora PS. Mini review: protein-protein interactions in transcription: a fertile ground for helix mimetics. Biopolymers. 5:1-7. Review. (2011)
Henchey LK, Porter JR, Ghosh I, Arora PS. High specificity in protein recognition by hydrogen-bond-surrogate α-helices: selective inhibition of the p53/MDM2 complex. Chembiochem. 18:2104-7. (2010)
Jochim AL, Arora PS. Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors. ACS Chem Biol. 5:919-23. (2010)
Patgiri A, Witten MR, Arora PS. Solid phase synthesis of hydrogen bond surrogate derived alpha-helices: resolving the case of a difficult amide coupling. Org Biomol Chem. 8:1773-6. (2010)
Tosovská P, Arora PS. Oligooxopiperazines as nonpeptidic alpha-helix mimetics.
Org Lett. 12:1588-91. (2010)
Joel Belasco:
Richards J, Liu Q, Pellegrini O, Celesnik H, Yao S, Bechhofer DH, Condon C, Belasco JG. An RNA pyrophosphohydrolase triggers 5'-exonucleolytic degradation of mRNA in Bacillus subtilis.
Mol Cell. 43:940-9. (2011)
Richards J, Belasco JG. Ribonuclease J: how to lead a double life. Structure. 19:1201-3. (2011)
Belasco JG. All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol. 11:467-78. (2010)
Savas JN, Ma B, Deinhardt K, Culver BP, Restituito S, Wu L, Belasco JG, Chao MV, Tanese N. A role for huntington disease protein in dendritic RNA granules. J Biol Chem. 285:13142-53.
Schuck A, Diwa A, Belasco JG. RNase E autoregulates its synthesis in Escherichia coli by binding directly to a stem-loop in the rne 5' untranslated region.
Mol Microbiol. 72:470-8. (2009)
Piao X, Zhang X, Wu L, Belasco JG. CCR4-NOT deadenylates mRNA associated with RNA-induced silencing complexes in human cells. Mol. Cell. Biol. 30:1486-1494 (2010)
Messing SAJ, Gabelli SB, Liu Q, Celesnik H, Belasco JG, Piñeiro SA, Amzel M. Structure and biological function of the RNA pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus. Structure 17:472-481 (2009)
Richard Bonneau:
Kirigin FF, Lindstedt K, Sellars M, Ciofani M, Low SL, Jones L, Bell F, Pauli F, Bonneau R, Myers RM, Littman DR, Chong MM. Dynamic microRNA gene transcription and processing during T cell development. J Immunol. 188:3257-67. (2012)
Paul B, Butterfoss GL, Boswell MG, Huang ML, Bonneau R, Wolf C, Kirshenbaum K. N-Naphthyl peptoid foldamers exhibiting atropisomerism. Org Lett. 14:926-9. (2012)
Poultney CS, Greenfield A, Bonneau R. Integrated inference and analysis of regulatory networks from multi-level measurements. Methods Cell Biol. 110:19-56. (2012)
Renfrew PD, Choi EJ, Bonneau R, Kuhlman B. Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. PLoS One. 7:e32637. (2012)
Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R. Comparative microbial modules resource: generation and visualization of multi-species biclusters. PLoS Comput Biol. 7:e1002228. (2011)
Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R. The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res. 21:1981-94. (2011)
Paul B, Butterfoss GL, Boswell MG, Renfrew PD, Yeung FG, Shah NH, Wolf C, Bonneau R, Kirshenbaum K. Peptoid Atropisomers. J Am Chem Soc. (2011)
Greenfield A, Madar A, Ostrer H, Bonneau R. DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. PLoS One. 5:e13397. (2010)
Madar A, Greenfield A, Vanden-Eijnden E, Bonneau R. DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. PLoS One. 5:e9803. (2010)
Jasna Brujic:
N. Biais, D. L. Higashi, J. Brujic, M. So, M.P. SheetzForce Dependent Polymorphism in Type IV Pili reveals Hidden Epitopes, PNAS, 2010 107, 25, 11358-11363
E. I. Corwin, M. Clusel, A. Siemens, J. Brujic, A model of random packing of polydisperse frictionless spheres, Soft Matter 2010 6, 2949-2959
Maxime Clusel, Eric I. Corwin, Alexander O. N. Siemens, Jasna Brujic, A 'granocentric' model for random packing of jammed emulsions, Nature, 30 July 2009, 460, 611-615
Sergi Garcia-Manyes, Lorna Dougan, Carmen L. Badilla, Jasna Brujic and Julio M. Fernandez, Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin, in Proceedings of the National Academy of Sciences (PNAS), May 12, 2009, 106, 26, 10534-10539, edited by Peter G. Wolynes, University of California at San Diego, La Jolla, CA
L.dougan, J. Brujic, J. M. Fernandez, Forceclamp spectroscopy of single proteins in Single Molecule Dynamics, in Life Sciences, 2008, edited by T. Yanagida and Y. Ishii,Wiley-VCH, Weinheim
S. Garcia-Manyes, J. Brujić, Carmen L. Badilla, and J.M. Fernandez, Force-clamp spectroscopy of single protein monomers reveals the individual unfolding and fodling pathways of I27 and ubiquitin, Biophys. J., 2007, doi:10.1529/biophysj.107.104422.
J. Brujić, C. Song, P. Wang, C. Briscoe, G. Marty, and H. A. Makse, Measuring the coordination number and entropy of a 3D jammed emulsion packing by confocal microscopy, Phys. Rev. Lett., 2007, 98, 248001.
J. Brujić, R. I. Z. Hermans, S. Garcia-Manyes, K. A. Walther, and J. M. Fernandez, Dwell-time distribution analysis of polyprotein unfolding using `force-clamp’ spectroscopy, Biophys. J., 2007, 92, 2896-2903.
S. R. K. Ainavarapu, J. Brujić, H. H. Huang, A. P. Wiita, H. Lu, L. Li, K. A. Walther, M. Carrion-Vazquez, H. Li, and J. M. Fernandez, Contour length and refolding rate of a small protein controlled by engineered disulfide bonds, Biophys. J., 2007, 92, 225-233.
J. Brujić, R. Hermans, K. A. Walther, J. M. Fernandez, Single molecule force spectroscopy reveals signatures of glassy dynamics in the energy landscape of ubiquitin, Nature Physics, 2006, 2, 282-286.
K. A. Walther, J. Brujić, H. Li, and J. M. Fernndez, Sub-angstrom conformational changes of a single molecule captured by AFM variance analysis, Biophys. J., 2006, 90, 3806-3812.
J. Brujić, D. Johnson, O. Sindt, H. A. Makse, Granular dynamics in compaction and stress relaxation, Phys. Rev. Lett., 2005, 128001.
S. F. Edwards, J. Brujić, H. A. Makse, edited by A. Coniglio, A. Fiero, H. J. Herrmann and M. Nicodemi, A basis for the statistical mechanics of granular systems in unifying concepts of granular media and glasses, Elsevier, 2004, Amsterdam.
J. Brujić, S. F. Edwards, D. V. Grinev, I. Hopkinson, D. Brujić, H. A. Makse, 3D bulk measurements of the force fistribution in a compressed emulsion system, Faraday Disc.,2003, 123, 207-220.
J. Brujić, S. F. Edwards, I. Hopkinson, and H. A. Makse, Measuring the distribution of interdroplet forces in a compressed emulsion system, Physica A, 2003, 327, 201-212.
J. Brujić, D. V. Grinev, S. F. Edwards, Jammed systems in slow flow need a new statistical mechanics, Proc. Roy. Soc. A, 2003, 361, 741.
S. F. Edwards, D. V. Grinev, J. Brujić, Fundamental problems in statistical physics of jammed packings, Physica A, 2003, 330, 61.
Tim Cardozo:
Almond D, Krachmarov C, Swetnam J, Zolla-Pazner S, Cardozo T. Resistance of Subtype C HIV-1 Strains to Anti-V3 Loop Antibodies. Adv Virol. 2012:803535. (2012)
Agarwal A, Hioe CE, Swetnam J, Zolla-Pazner S, Cardozo T. Quantitative assessment of masking of neutralization epitopes in HIV-1. Vaccine. 29:6736-41. (2011)
Gonsalves FC, Klein K, Carson BB, Katz, S, Ekas LA, Evans S, Nagourney R, Cardozo T, Brown AMC, Dasgupta R.Feature Article: From the Cover: An RNAi-based chemical genetic screen identifies three small-molecule inhibitors of the Wnt/wingless signaling pathway. Proceedings of the National Academy of Sciences of the United States of America. 108:5954-63 (2011)
Agarwal, A, Swetnam J, Zolla-Pazner S, Cardozo, T. Quantitative Assessment of HIV-1 Neutralization Epitope Masking. AIDS research & human retroviruses. 26:A74-A74. (2010)
Almond D, Kong X, Zolla-Pazner S, Cardozo T.Map of broad and narrow neutralization in the V3 loop crown AIDS research & human retroviruses. 26:A27-A28. (2010)
Almond D, Kimura T, Kong X, Swetnam,J, Zolla-Pazner S, Cardozo T. Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop. AIDS research & human retroviruses. 26:717-23. (2010)
Band PA, Blais S, Neubert T, Cardozo T, Ichtchenko K. Recombinant derivatives of botulinum neurotoxin A engineered for trafficking studies and neuronal delivery. Protein expression & purification. 71:62-73. (2010)
Cardozo T, Kong X, Totrov M, Wang S, Lu S., Gorny M, Pinter A, Seaman M, Zolla-Pazner S. Engineered immunogen presenting an epitope recognized by a neutralizing mAb elicits mammalian serum that recapitulate the mAb's specificity. AIDS research & human retroviruses. 26:A26-A27, (2010)
Ekas L, Cardozo T, Flaherty M, McMillan E, Gonsalves F, Bach E. Characterization of a dominant-active STAT that promotes tumorigenesis in Drosophila.Developmental biology. 344:621-36. (2010)
Goyanka, R, Das S, Samuels H, Cardozo T. Nuclear receptor engineering based on novel structure activity relationships revealed by farnesyl pyrophosphate. Protein engineering, design & selection : PEDS. 23:809-15. (2010)
Jiang X, Burke V, Totrov M, Williams C, Cardozo T, Gorny MK, Zolla-Pazner S, Kong X. Conserved structural elements in the V3 crown of HIV-1 gp120. Nature structural & molecular biology. 17:955-61. (2010)
Michael Dustin:
Dustin ML, Groves JT. Receptor signaling clusters in the immune synapse. Annu Rev Biophys. 41:543-56. (2012)
Dustin ML. Signaling at neuro/immune synapses. J Clin Invest. 122:1149-55. (2012)
Prins KC, Vasiliver-Shamis G, Cammer M, Depoil D, Dustin ML, Hioe CE. Imaging of HIV-1 envelope-induced virological synapse and signaling on synthetic lipid bilayers. J Vis Exp. (2012)
Zanin-Zhorov A, Lin J, Scher J, Kumari S, Blair D, Hippen KL, Blazar BR, Abramson SB, Lafaille JJ, Dustin ML. Scaffold protein Disc large homolog 1 is required for T-cell receptor-induced activation of regulatory T-cell function. Proc Natl Acad Sci USA. 109:1625-30. (2012)
Dustin ML, Meyer-Hermann M. Immunology. Antigen feast or famine. Science. 335:408-9. (2012)
Dustin ML, Depoil D. New insights into the T cell synapse from single molecule techniques.
Nat Rev Immunol. 11:672-84. (2011)
Zanin-Zhorov A, Dustin ML, Blazar BR. PKC-θ function at the immunological synapse: prospects for therapeutic targeting. Trends Immunol. (2011)
Waite JC, Leiner I, Lauer P, Rae CS, Barbet G, Zheng H, Portnoy DA, Pamer EG, Dustin ML. Dynamic imaging of the effector immune response to listeria infection in vivo. PLoS Pathog. 7:e1001326. (2011)
Tang W, Lu Y, Tian QY, Zhang Y, Guo FJ, Liu GY, Syed NM, Lai Y, Lin EA, Kong L, Su J, Yin F, Ding AH, Zanin-Zhorov A, Dustin ML, Tao J, Craft J, Yin Z, Feng JQ, Abramson SB, Yu XP, Liu CJ. The growth factor progranulin binds to TNF receptors and is therapeutic against inflammatory arthritis in mice. Science. 332:478-84. (2011)
Vasiliver-Shamis G, Dustin ML, Hioe CE. HIV-1 Virological Synapse is not Simply a Copycat of the Immunological Synapse. Viruses. 2:1239-1260. (2010)
Dustin ML, Chakraborty AK, Shaw AS. Understanding the structure and function of the immunological synapse. Cold Spring Harb Perspect Biol. 2:a002311. (2010)
Fooksman DR, Schwickert TA, Victora GD, Dustin ML, Nussenzweig MC, Skokos D.
Development and migration of plasma cells in the mouse lymph node. Immunity. 33:118-27. (2010)
Stevan Hubbard:
Zhang W, Coldefy AS, Hubbard SR, Burden SJ. Agrin binds to the N-terminal region of Lrp4 protein and stimulates association between Lrp4 and the first immunoglobulin-like domain in muscle-specific kinase (MuSK). J Biol Chem. 286:40624-30. (2011)
Hubbard SR. Cytokine signaling exposed. Structure. 19:1-2. (2011)
Jamieson KV, Hubbard SR, Meruelo D. Structure-guided identification of a laminin binding site on the laminin receptor precursor. J Mol Biol. 405:24-32. (2011)
Cerda-Maira FA, Pearce MJ, Fuortes M, Bishai WR, Hubbard SR, Darwin KH. Molecular analysis of the prokaryotic ubiquitin-like protein (Pup) conjugation pathway in Mycobacterium tuberculosis. Mol Microbiol. 77:1123-35. (2010)
Bergamin E, Hallock PT, Burden SJ, Hubbard SR. The cytoplasmic adaptor protein Dok7 activates the receptor tyrosine kinase MuSK via dimerization. Mol Cell. 39:100-9. (2010)
Stiegler AL, Burden SJ, Hubbard SR. Crystal structure of the frizzled-like cysteine-rich domain of the receptor tyrosine kinase MuSK. J Mol Biol. 393:1-9. (2009)
Depetris RS, Wu J, Hubbard SR. Structural and functional studies of the Ras-associating and pleckstrin-homology domains of Grb10 and Grb14. Nat Struct Mol Biol. 16:833-9. (2009)
Hubbard SR. The juxtamembrane region of EGFR takes center stage. Cell. 137:1181-3. (2009)
Michelle Krogsgaard:
Zhong S, Malecek K, Perez-Garcia A, Krogsgaard M. Retroviral transduction of T-cell receptors in mouse T-cells. J Vis Exp. (2010)
Wich L, Hamilton H, Shapiro R, Pavlick A, Berman R, Polsky D, Goldberg J, Hernando E, Manga P, Krogsgaard M, Kamino H, Darvishian F, Lee P, Orlow S, Ostrer H, Bhardwaj N, Osman I. Developing a multidisciplinary prospective melanoma biospecimen repository to advance translational research. American Journal of Translational Research. 1:35-43 (2009)
Call MJ, Xing XC, Cuny GD, Seth NP, Altmann DM, Fugger L, Krogsgaard M, Stein RL, Wucherpfennig KW. In Vivo Enhancement of Peptide Display by MHC Class II Molecules with Small Molecule Catalysts of Peptide Exchange. Journal of immunology. 182:6342-6352. (2009)
Zhong S, Malecek K, Perez-Garcia A, Krogsgaard M. Retroviral Transduction of T-cell Receptors in Mouse T-cells. Journal of visualized experiments. (2010)
Mouquet H, Scheid J, Zoller M, Krogsgaard M, Ott R, Shukair S, Artyomov M, Pietzsch J, Connors M, Pereyra F, Walker B, Ho D, Wilson P, Seaman M, Eisen H, Chakraborty A, Hope T, Ravetch J, Wardemann H, Nussenzweig M. Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature. 467:591-5. (2010)
Juang J, Ebert P, Feng D, Garcia C, Krogsgaard M, Davis M. Peptide-MHC heterodimers show that thymic positive selection requires a more restricted set of self-peptides than negative selection. Journal of experimental medicine. 207:1223-1234. (2010)
Corse E, Gottschalk R, Krogsgaard M, Allison J. Attenuated T cell responses to a high-potency ligand in vivo. L. PLoS biology. 8:e1000481. (2010)
Xiangpeng Kong:
Almond D, Kimura T, Kong X, Swetnam J, Zolla-Pazner S, Cardozo T. Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop. AIDS Res Hum Retroviruses. 26:717-23. (2010)
Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, Salomon A, Williams C, Seaman MS, Abagyan R, Cardozo T, Gorny MK, Wang S, Lu S, Pinter A, Zolla-Pazner S. Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology. 405:513-23. (2010)
Jiang X, Burke V, Totrov M, Williams C, Cardozo T, Gorny MK, Zolla-Pazner S, Kong XP. Conserved structural elements in the V3 crown of HIV-1 gp120. Nat. Struct. Mol. Biol. 17: 955-61. (2010)
Li HG, Huang PL, Zhang D, Sun Y, Chen HC, Zhang J, Huang PL, Kong XP, Lee-Huang S. A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase--structural and modeling insight into its functions. Biochem. Biophys. Res. Commun. 391:340-5. (2010)
Burke V, Williams C, Sukumaran M, Kim SS, Li H, Wang XH, Gorny MK, Zolla-Pazner S, Kong XP. Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens. Structure. 17:1538-46. (2009)
Ubeda C, Olivarez NP, Barry P, Wang H, Kong X, Matthews A, Tallent SM, Christie GE, Novick RP. Specificity of staphylococcal phage and SaPI DNA packaging as revealed by integrase and terminase mutations. Mol Microbiol. 2009 72:98-108. (2009)
Liu Z, Gosser Y, Baker PJ, Ravee Y, Lu Z, Alemu G, Li H, Butterfoss GL, Kong XP, Gross R, Montclare JK. Structural and functional studies of Aspergillus oryzae cutinase: enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation. J. Am. Chem. Soc.131:15711-6. (2009)
Wang H, Min G, Glockshuber R, Sun TT, Kong XP. Uropathogenic E. coli adhesin-induced host cell receptor conformational changes: implications in transmembrane signaling transduction. J. Mol. Biol.392:352-61. (2009)
Jaglin XH, Poirier K, Saillour Y, Buhler E, Tian G, Bahi-Buisson N, Fallet-Bianco C, Phan-Dinh-Tuy F, Kong XP, Bomont P, Castelnau-Ptakhine L, Odent S, Loget P, Kossorotoff M, Snoeck I, Plessis G, Parent P, Beldjord C, Cardoso C, Represa A, Flint J, Keays DA, Cowan NJ, Chelly J. Nat. Genet. 41:746-52. (2009)
Wu XR, Kong XP, Pellicer A, Kreibich G, Sun TT. Uroplakins in urothelial biology, function, and disease. Kidney Int. 75:1153-65. (2009)
Moosa Mohammadi:
Goetz R, Ohnishi M, Ding X, Kurosu H, Wang L, Akiyoshi J, Ma J, Gai W, Sidis Y, Pitteloud N, Kuro-O M, Razzaque MS, Mohammadi M. Klotho coreceptors inhibit signaling by paracrine fibroblast growth factor 8 subfamily ligands. Mol Cell Biol. 32:1944-54. (2012)
Beenken A, Mohammadi M. The structural biology of the FGF19 subfamily. Adv Exp Med Biol. 2012 728:1-24. (2012)
Zhou H, Huang HY, Shapiro E, Lepor H, Huang WC, Mohammadi M, Mohr I, Tang MS, Huang C, Wu XR. Urothelial tumor initiation requires deregulation of multiple signaling pathways: implications in target-based therapies. Carcinogenesis. 33:770-80. (2012)
Kalinina J, Dutta K, Ilghari D, Beenken A, Goetz R, Eliseenkova AV, Cowburn D, Mohammadi M. The alternatively spliced acid box region plays a key role in FGF receptor autoinhibition. Structure. 20:77-88. (2012)
Beenken A, Eliseenkova AV, Ibrahimi OA, Olsen SK, Mohammadi M. Plasticity in interactions of fibroblast growth factor 1 (FGF1) N terminus with FGF receptors underlies promiscuity of FGF1. J Biol Chem. 287:3067-78. (2012)
Goetz R, Nakada Y, Hu MC, Kurosu H, Wang L, Nakatani T, Shi M, Eliseenkova AV, Razzaque MS, Moe OW, Kuro-o M, Mohammadi M. Isolated C-terminal tail of FGF23 alleviates hypophosphatemia by inhibiting FGF23-FGFR-Klotho complex formation. Proc Natl Acad Sci USA. 107:407-12. (2010)
Kalinina J, Byron SA, Makarenkova HP, Olsen SK, Eliseenkova AV, Larochelle WJ, Dhanabal M, Blais S, Ornitz DM, Day LA, Neubert TA, Pollock PM, Mohammadi M. Homodimerization controls the fibroblast growth factor 9 subfamily's receptor binding and heparan sulfate-dependent diffusion in the extracellular matrix. Mol Cell Biol. 29:4663-78. (2009)
Goetz R, Dover K, Laezza F, Shtraizent N, Huang X, Tchetchik D, Eliseenkova AV, Xu CF, Neubert TA, Ornitz DM, Goldfarb M, Mohammadi M. Crystal structure of a fibroblast growth factor homologous factor (FHF) defines a conserved surface on FHFs for binding and modulation of voltage-gated sodium channels. J Biol Chem. 284:17883-96. (2009)
Beenken A, Mohammadi M. The FGF family: biology, pathophysiology and therapy.
Nat Rev Drug Discov. 8:235-53. (2009)
Thomas Neubert:
Schlame M, Blais S, Edelman-Novemsky I, Xu Y, Montecillo F, Phoon CK, Ren M, Neubert TA. Comparison of cardiolipins from Drosophila strains with mutations in putative remodeling enzymes.
Chem Phys Lipids. 165:512-519. (2012)
Zhou G, Liang FX, Romih R, Wang Z, Liao Y, Ghiso J, Luque-Garcia JL, Neubert TA, Kreibich G, Alonso MA, Schaeren-Wiemers N, Sun TT. MAL facilitates the incorporation of exocytic uroplakin-delivering vesicles into the apical membrane of urothelial umbrella cells. Mol Biol Cell. 23:1354-66. (2012)
Zhang G, Neubert TA, Jordan BA. RNA binding proteins accumulate at the postsynaptic density with synaptic activity. J Neurosci. 32:599-609. (2012)
Deinhardt K, Kim T, Spellman DS, Mains RE, Eipper BA, Neubert TA, Chao MV, Hempstead BL. Neuronal growth cone retraction relies on proneurotrophin receptor signaling through Rac. Sci Signal. 4:ra82. (2011)
Zhang G, Neubert TA. Comparison of three quantitative phosphoproteomic strategies to study receptor tyrosine kinase signaling. J Proteome Res. 10:5454-62. (2011)
Hong M, Kefaloyianni E, Bao L, Malester B, Delaroche D, Neubert TA, Coetzee WA. Cardiac ATP-sensitive K+ channel associates with the glycolytic enzyme complex. FASEB J. 25:2456-67. (2011)
Yeung KT, Das S, Zhang J, Lomniczi A, Ojeda SR, Xu CF, Neubert TA, Samuels HH. A novel transcription complex that selectively modulates apoptosis of breast cancer cells through regulation of FASTKD2. Mol Cell Biol. 31:2287-98. (2011)
Zito E, Melo EP, Yang Y, Wahlander Å, Neubert TA, Ron D. Oxidative protein folding by an endoplasmic reticulum-localized peroxiredoxin. Mol Cell. 40:787-97. (2010)
Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, Reinberg D. Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev. 24:2615-20. (2010)
Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. Curr Protoc Protein Sci.16:Unit16.1. (2010)
Hallock PT, Xu CF, Park TJ, Neubert TA, Curran T, Burden SJ. Dok-7 regulates neuromuscular synapse formation by recruiting Crk and Crk-L. Genes Dev. 24:2451-61. (2010)
Zhang G, Ueberheide BM, Waldemarson S, Myung S, Molloy K, Eriksson J, Chait BT, Neubert TA, Fenyö D. Protein quantitation using mass spectrometry. Methods Mol Biol. 673:211-22. (2010)
Evgeny Nudler:
Gusarov I, Nudler E. S-Nitrosylation Signaling in Escherichia coli. Sci Signal. 5:26. (2012)
Svetlov V, Artsimovitch I, Nudler E. Response to Klyuyev and Vassylyev: on the mechanism of tagetitoxin inhibition of transcription. Transcription. 3:51-5. (2012)
Shatalin K, Shatalina E, Mironov A, Nudler E. H2S: a universal defense against antibiotics in bacteria. Science. 334:986-90. (2011)
Dutta D, Shatalin K, Epshtein V, Gottesman ME, Nudler E. Linking RNA polymerase backtracking to genome instability in E. coli. Cell. 146:533-43. (2011)
Svetlov V, Nudler E. Clamping the clamp of RNA polymerase. EMBO J. 30:1190-1. (2011)
Proshkin S, Rahmouni AR, Mironov A, Nudler E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science. 328:504-8. (2010)
Epshtein V, Dutta D, Wade J, Nudler E. An allosteric mechanism of Rho-dependent transcription termination. Nature. 463:245-9. (2010)
Svetlov V, Nudler E. Macromolecular micromovements: how RNA polymerase translocates. Curr Opin Struct Biol. 19:701-7. (2009)
Eli Rothenberg:
Chkourko HS, Guerrero-Serna G, Lin X, Darwish N, Pohlmann JR, Cook KE, Martens JR, Rothenberg E, Musa H, Delmar M. Remodeling of mechanical junctions and of microtubule-associated proteins accompany cardiac connexin 43 lateralization. Heart Rhythm. (2012)
Rothenberg E, Sepúlveda LA, Skinner SO, Zeng L, Selvin PR, Golding I. Single-virus tracking reveals a spatial receptor-dependent search mechanism. Biophys J. 100:2875-82. (2011)
Rothenberg E, Ha T. Single-molecule FRET analysis of helicase functions. Methods Mol Biol. 587:29-43. (2010)
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Nadrian Seeman:
Nguyen N, Birktoft JJ, Sha R, Wang T, Zheng J, Constantinou PE, Ginell SL, Chen Y, Mao C, Seeman NC. The absence of tertiary interactions in a self-assembled DNA crystal structure. J Mol Recognit. 25:234-7. (2012)
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Baas NA, Seeman NC. ON THE CHEMICAL SYNTHESIS OF NEW TOPOLOGICAL STRUCTURES. J Math Chem. :220-232. (2012)
Wang T, Sha R, Dreyfus R, Leunissen ME, Maass C, Pine DJ, Chaikin PM, Seeman NC. Self-replication of information-bearing nanoscale patterns. Nature. 478:225-8. (2011)
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Alexander Serganov:
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Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA. 18:610-25. (2012)
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David Stokes:
Ubarretxena-Belandia I, Stokes DL. Membrane protein structure determination by electron crystallography. Curr Opin Struct Biol. (2012)
Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure. 20:205-14. (2012)
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Leo-Macias A, Katz G, Wei H, Alimova A, Katz A, Rice WJ, Diaz-Avalos R, Hu GB, Stokes DL, Gottlieb P. Toroidal surface complexes of bacteriophage ϕ12 are responsible for host-cell attachment. Virology. 414:103-9. (2011)
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Nate Traaseth:
Banigan JR, Traaseth NJ. Using Afterglow Magnetization from Cross-Polarization Magic-Angle-Spinning Solid-State NMR Spectroscopy to Obtain Simultaneous Heteronuclear Multidimensional Spectra. J Phys Chem B. (2012) [pdf]
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Daniel Turnbull:
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Da-Neng Wang:
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Yingkai Zhang:
Wu R, Lu Z, Cao Z, Zhang Y. A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins. J Chem Theory Comput. 7:433-443. (2011)
Zhou Y, Zhang Y. Serine protease acylation proceeds with a subtle re-orientation of the histidine ring at the tetrahedral intermediate. Chem Commun (Camb). 47:1577-9. (2011)
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